Daniel Podlesny
@podlesny.bsky.social
Postdoc @BorkLab.bsky.social @embl.org. PhD @UniHohenheim.bsky.social. Microbiome, HGT, FMT, Strain-level Metagenomics
Pinned
Daniel Podlesny
@podlesny.bsky.social
· Dec 2
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Reposted by Daniel Podlesny
I am pleased to share that our paper is now published in Cell!
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.
This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.
This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.
February 9, 2026 at 9:07 PM
I am pleased to share that our paper is now published in Cell!
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.
This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.
This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.
Reposted by Daniel Podlesny
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex...
See the quoted post below for a thread on the preprint!
See the quoted post below for a thread on the preprint!
February 9, 2026 at 5:08 PM
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex...
See the quoted post below for a thread on the preprint!
See the quoted post below for a thread on the preprint!
Reposted by Daniel Podlesny
In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠
🔗 Read more here: www.embl.org/news/science...
🔗 Read more here: www.embl.org/news/science...
February 9, 2026 at 4:42 PM
In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠
🔗 Read more here: www.embl.org/news/science...
🔗 Read more here: www.embl.org/news/science...
Reposted by Daniel Podlesny
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 30, 2026 at 3:05 PM
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
Reposted by Daniel Podlesny
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Daniel Podlesny
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 22, 2026 at 7:40 AM
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
Reposted by Daniel Podlesny
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:01 PM
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Reposted by Daniel Podlesny
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
metaTraits: a large-scale integration of microbial phenotypic trait information
Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is
academic.oup.com
November 30, 2025 at 4:47 AM
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
December 2, 2025 at 5:52 PM
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Reposted by Daniel Podlesny
Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Alcohol-related liver disease disrupts bile acid synthesis and is associated with compensatory gut microbiota changes
Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids...
www.medrxiv.org
July 24, 2025 at 5:02 PM
Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Daniel Podlesny
New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!
#MicroSky 🖥️🧬🦠
#MicroSky 🖥️🧬🦠
Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...
www.biorxiv.org
July 21, 2025 at 1:57 PM
New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!
#MicroSky 🖥️🧬🦠
#MicroSky 🖥️🧬🦠
Reposted by Daniel Podlesny
Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...
www.biorxiv.org
July 21, 2025 at 11:56 AM
Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
Reposted by Daniel Podlesny
The team's first preprint is out!
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
The team's first preprint is out!
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
Reposted by Daniel Podlesny
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
June 25, 2025 at 7:25 PM
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Reposted by Daniel Podlesny
Europe’s choice is clear.
To put science at the heart of its economy.
To become the home of scientific freedom and collaboration.
And to welcome talent from all over the world.
I’m glad to present the first elements of our Choose Europe Initiative.
→ europa.eu/!TTbWbJ
To put science at the heart of its economy.
To become the home of scientific freedom and collaboration.
And to welcome talent from all over the world.
I’m glad to present the first elements of our Choose Europe Initiative.
→ europa.eu/!TTbWbJ
May 5, 2025 at 10:00 AM
Europe’s choice is clear.
To put science at the heart of its economy.
To become the home of scientific freedom and collaboration.
And to welcome talent from all over the world.
I’m glad to present the first elements of our Choose Europe Initiative.
→ europa.eu/!TTbWbJ
To put science at the heart of its economy.
To become the home of scientific freedom and collaboration.
And to welcome talent from all over the world.
I’m glad to present the first elements of our Choose Europe Initiative.
→ europa.eu/!TTbWbJ
Live in 2h: Metagenomic microbial strain tracking in the cloud! I'll be doing a quick demo showing how to use the SameStr workflow on the @nfdi4microbiota.bsky.social Cloud-based Workflow Platform (CloWM) - GUI / no-install / scalable / free for scientific use.
Join our next Coffee Talk on 28 April at 14:30 CEST!
@podlesny.bsky.social (EMBL) presents SameStr—a new tool for strain-resolved metagenomics. Track microbes with high precision.
🔗 Zoom: ID 687 6408 9023 | PW: 826218
#Microbiome #Metagenomics #OpenScience
@podlesny.bsky.social (EMBL) presents SameStr—a new tool for strain-resolved metagenomics. Track microbes with high precision.
🔗 Zoom: ID 687 6408 9023 | PW: 826218
#Microbiome #Metagenomics #OpenScience
April 28, 2025 at 10:21 AM
Live in 2h: Metagenomic microbial strain tracking in the cloud! I'll be doing a quick demo showing how to use the SameStr workflow on the @nfdi4microbiota.bsky.social Cloud-based Workflow Platform (CloWM) - GUI / no-install / scalable / free for scientific use.
Reposted by Daniel Podlesny
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Reposted by Daniel Podlesny
Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder.
datajournal.org/schon-wieder/
datajournal.org/schon-wieder/
Schon wieder
Der Aufstieg der NSDAP/AfD
datajournal.org
February 20, 2025 at 9:41 AM
Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder.
datajournal.org/schon-wieder/
datajournal.org/schon-wieder/
Reposted by Daniel Podlesny
Dass nur eine einzige Redaktion sich hier traut, zu schreiben, was jeder sehen konnte: "Musk macht Hitlergruß" – das ist so dystopisch, ihr werft uns denen zum Fraß vor.
January 21, 2025 at 5:59 AM
Dass nur eine einzige Redaktion sich hier traut, zu schreiben, was jeder sehen konnte: "Musk macht Hitlergruß" – das ist so dystopisch, ihr werft uns denen zum Fraß vor.
Reposted by Daniel Podlesny
Die deutschen Mainstream-Medien sind soweit nach links gerutscht, dass sie einen Hitlergruß nicht mehr Hitlergruß nennen.
January 21, 2025 at 7:18 AM
Die deutschen Mainstream-Medien sind soweit nach links gerutscht, dass sie einen Hitlergruß nicht mehr Hitlergruß nennen.
Reposted by Daniel Podlesny
NEW ONLINE! New online! A phylogenetic approach to comparative genomics
A phylogenetic approach to comparative genomics
Nature Reviews Genetics, Published online: 08 January 2025; doi:10.1038/s41576-024-00803-0Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests.…
go.nature.com
January 8, 2025 at 1:58 PM
NEW ONLINE! New online! A phylogenetic approach to comparative genomics
Reposted by Daniel Podlesny
I’m excited to share our new paper published in Nature Communications!
In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups.
www.nature.com/articles/s41...
In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups.
www.nature.com/articles/s41...
A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy - Nature Communications
Here, the authors show that higher levels of the gut bacterial clade TANB77 associate with better response to cancer immunotherapy, and further demonstrate in mice that a conserved pilin from TANB77 p...
www.nature.com
December 28, 2024 at 1:57 PM
I’m excited to share our new paper published in Nature Communications!
In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups.
www.nature.com/articles/s41...
In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups.
www.nature.com/articles/s41...
Reposted by Daniel Podlesny
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses
Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...
www.biorxiv.org
December 23, 2024 at 7:29 AM
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
Reposted by Daniel Podlesny
🚨 New review in @natrevgastrohep.bsky.social:
Should you take probiotics with antibiotics?
www.nature.com/articles/s41...
Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵
Should you take probiotics with antibiotics?
www.nature.com/articles/s41...
Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵
December 13, 2024 at 11:34 PM
🚨 New review in @natrevgastrohep.bsky.social:
Should you take probiotics with antibiotics?
www.nature.com/articles/s41...
Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵
Should you take probiotics with antibiotics?
www.nature.com/articles/s41...
Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵
Reposted by Daniel Podlesny
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
December 11, 2024 at 4:29 PM
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55